Calculation of the distribution of peaks into different genome gene features.

> bin/genomeDistribution -h
SeqCode_v1.0		 			User commands				    genomeDistribution

NAME
	genomeDistribution - a program to examine the distribution of peaks within distinct genomic features.

SYNOPSIS
	genomeDistribution [-1/7 ][-d][-g ][-p 1234][-q 12][-s ][-w ][-v][-x prefix][-h]
	   

OUTPUT
	One folder with 3 files:
	- Peaks associated to genomic regions
	- R script commands
	- Graphical representation (R is required).

OPTIONS
	-1 : Color 1, Distal/Promoter (default: coral).
	-2 : Color 2, Proximal/Intragenic (default: darkred).
	-3 : Color 3, 5'UTR/Intergenic (default: burlywood).
	-4 : Color 4, 3'UTR (default: orchid).
	-5 : Color 5, CDS (default: chartreuse3).
	-6 : Color 6, Introns (default: gold).
	-7 : Color 7, Intergenic (default: corflowerblue).
	-d : Detailed analysis with introns/exons/promoters.
	-g : Gradient palette from Color1 to white.
	-p : Viridis palettes (1=viridis|2=magma|3=plasma|4=inferno).
	-q : ColorBrewer palettes (1=accent|2=paired).
	-s : Simplified with genic/intragenic/intergenic (X bp around TSS).
	-w : Window resolution (default: 100).
	-v : Verbose. Display info messages.
	-x : Prefix for the output folder.
	-h : Show this help.

SEE ALSO
    SeqCode homepage: http://ldicrocelab.crg.es
    GitHub source code: https://github.com/eblancoga/seqcode

AUTHORS
	Written by Enrique Blanco.

SeqCode_v1.0					User commands					genomeDistribution

Example 1. How to generate a comprehensive pie chart with the full set of genomic features.

> bin/genomeDistribution -vd ChromInfo.txt refGene.txt H3K4me3_peaks.bed H3K4me3_detail

Example 2. How to colorize the piechart with the ColorBrewer accent palette.

> bin/genomeDistribution -vdq 1 ChromInfo.txt refGene.txt H3K4me3_peaks.bed H3K4me3_accent

Example 3. How to colorize the piechart with the ColorBrewer paired palette.

> bin/genomeDistribution -vdq 2 ChromInfo.txt refGene.txt H3K4me3_peaks.bed H3K4me3_paired

Example 4. How to colorize the piechart with the Viridis palette.

> bin/genomeDistribution -vdp 1 ChromInfo.txt refGene.txt H3K4me3_peaks.bed H3K4me3_viridis

Example 5. How to colorize the piechart with the Viridis magma palette.

> bin/genomeDistribution -vdp 2 ChromInfo.txt refGene.txt H3K4me3_peaks.bed H3K4me3_magma

Example 6. How to colorize the piechart with the Viridis plasma palette.

> bin/genomeDistribution -vdp 3 ChromInfo.txt refGene.txt H3K4me3_peaks.bed H3K4me3_plasma

Example 7. How to colorize the piechart with the Viridis inferno palette.

> bin/genomeDistribution -vdp 4 ChromInfo.txt refGene.txt H3K4me3_peaks.bed H3K4me3_inferno

Example 8. How to colorize the piechart with the colors selected by the user.

> bin/genomeDistribution -vd -1 darkred -2 darkorange -3 yellow -4 darkgreen -5 darkblue -6 magenta -7 violet ChromInfo.txt refGene.txt H3K4me3_peaks.bed H3K4me3_customized

Example 9. How to colorize the piechart with a gradient of colors.

> bin/genomeDistribution -vd -g -1 darkred $MOUSE9/ChromInfo.txt $MOUSE9/refGene.txt H3K4me3_peaks.bed H3K4me3_gradient

Example 10. How to generate a simplified piechart focusing on only three classes customized by distance to TSS.

> bin/genomeDistribution -vs 2500 -1 darkblue -2 grey -3 white ChromInfo.txt refGene.txt H3K4me3_peaks.bed H3K4me3_simplified

Example 11. How to generate a simple pie chart with the basic gene features (not defined by distance to TSS).

> bin/genomeDistribution -v ChromInfo.txt refGene.txt H3K4me3_peaks.bed H3K4me3_basic

Please, note that peaks overlapping more than one genomic feature are proportionally counted the same number of times. The original number of peaks and the resulting number of peaks after the application of this rule are included into the caption of resulting plots.

Please, follow the link below for further information on how to get and preprocess the raw data of published ChIPseq and RNAseq samples utilized in this glossary of SeqCode functions.

[SAMPLES]